To change your guards, simply talk to the appropriate faction officer in your Town Hall. You won't see officers for factions you aren't exalted with. On the beta I'm only exalted with the Exodar, so the only officer standing in my Town Hall was a draenei named Officer Torluun, who offered me the option to have the draenei come protect my garrison if I wanted it done. I gave him the word, went outside, and every guard in the place had changed to the guards shown above. At the present time, there doesn't seem to be a way to change the guards back to human -- but I'm not exalted with Stormwind, so it may simply be a matter of grinding the reputation out.
Currently, it seems as though the option is not available for Horde garrisons, but I'm sure it will be added in due time. Although the garrison guards are nothing more than a visual preference, I think this is the first time it's ever felt like those old vanilla reputations had some weight and impact in the game. Sure, they may not do anything substantial, but I'm glad I can call on the allies I've helped out time and time again, and give my garrison some additional flavor while I'm at it.